Starting phenix.real_space_refine on Sun Feb 8 07:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo9_61648/02_2026/9jo9_61648.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo9_61648/02_2026/9jo9_61648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jo9_61648/02_2026/9jo9_61648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo9_61648/02_2026/9jo9_61648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jo9_61648/02_2026/9jo9_61648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo9_61648/02_2026/9jo9_61648.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 16710 2.51 5 N 4320 2.21 5 O 5010 1.98 5 H 15920 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42040 Number of models: 1 Model: "" Number of chains: 20 Chain: "O" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "S" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "F" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "K" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "M" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "P" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "Q" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "R" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "T" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Time building chain proxies: 7.14, per 1000 atoms: 0.17 Number of scatterers: 42040 At special positions: 0 Unit cell: (120.555, 119.7, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 5010 8.00 N 4320 7.00 C 16710 6.00 H 15920 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS O 24 " - pdb=" SG CYS O 98 " distance=2.69 Simple disulfide: pdb=" SG CYS S 36 " - pdb=" SG CYS S 97 " distance=2.34 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.38 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.31 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.36 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 98 " distance=2.22 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 97 " distance=2.39 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 98 " distance=2.31 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.35 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 98 " distance=2.37 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 97 " distance=2.35 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 98 " distance=2.34 Simple disulfide: pdb=" SG CYS L 36 " - pdb=" SG CYS L 97 " distance=2.35 Simple disulfide: pdb=" SG CYS N 36 " - pdb=" SG CYS N 97 " distance=2.34 Simple disulfide: pdb=" SG CYS P 24 " - pdb=" SG CYS P 98 " distance=2.40 Simple disulfide: pdb=" SG CYS Q 36 " - pdb=" SG CYS Q 97 " distance=2.35 Simple disulfide: pdb=" SG CYS T 36 " - pdb=" SG CYS T 97 " distance=2.35 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6020 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 50 sheets defined 6.8% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'O' and resid 30 through 34 Processing helix chain 'S' and resid 43 through 46 Processing helix chain 'S' and resid 167 through 177 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.730A pdb=" N SER B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.580A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'D' and resid 42 through 46 removed outlier: 4.178A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.856A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.934A pdb=" N SER F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'H' and resid 167 through 177 Processing helix chain 'I' and resid 30 through 34 Processing helix chain 'J' and resid 43 through 46 Processing helix chain 'J' and resid 167 through 177 Processing helix chain 'K' and resid 30 through 34 Processing helix chain 'L' and resid 43 through 46 Processing helix chain 'L' and resid 167 through 177 Processing helix chain 'M' and resid 30 through 34 Processing helix chain 'N' and resid 42 through 46 removed outlier: 3.900A pdb=" N SER N 45 " --> pdb=" O GLU N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 177 Processing helix chain 'N' and resid 186 through 190 removed outlier: 3.753A pdb=" N LEU N 190 " --> pdb=" O TRP N 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 34 Processing helix chain 'Q' and resid 167 through 177 Processing helix chain 'Q' and resid 186 through 190 removed outlier: 3.928A pdb=" N LEU Q 190 " --> pdb=" O TRP Q 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 34 Processing helix chain 'T' and resid 42 through 46 removed outlier: 3.849A pdb=" N SER T 45 " --> pdb=" O GLU T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 177 Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.747A pdb=" N LEU T 190 " --> pdb=" O TRP T 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'O' and resid 12 through 15 removed outlier: 6.333A pdb=" N GLY O 12 " --> pdb=" O THR O 125 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N SER O 127 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL O 14 " --> pdb=" O SER O 127 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER O 101 " --> pdb=" O TYR O 35 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR O 35 " --> pdb=" O SER O 101 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET O 36 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER O 52 " --> pdb=" O MET O 36 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP O 38 " --> pdb=" O VAL O 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 114 through 115 Processing sheet with id=AA4, first strand: chain 'S' and resid 114 through 115 removed outlier: 3.943A pdb=" N ILE S 106 " --> pdb=" O GLU S 101 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS S 38 " --> pdb=" O ASN S 158 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN S 158 " --> pdb=" O HIS S 38 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR S 40 " --> pdb=" O ILE S 156 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE S 156 " --> pdb=" O TYR S 40 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE S 156 " --> pdb=" O PHE S 9 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN S 158 " --> pdb=" O LYS S 7 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N LYS S 7 " --> pdb=" O ASN S 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 80 through 85 removed outlier: 5.972A pdb=" N ASN S 61 " --> pdb=" O THR S 56 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR S 56 " --> pdb=" O ASN S 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE S 52 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP S 67 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER S 50 " --> pdb=" O TRP S 67 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE S 133 " --> pdb=" O LEU S 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 5 through 9 Processing sheet with id=AA7, first strand: chain 'A' and resid 12 through 15 removed outlier: 6.318A pdb=" N GLY A 12 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER A 127 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 14 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET A 36 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER A 52 " --> pdb=" O MET A 36 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP A 38 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 61 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 120 removed outlier: 4.523A pdb=" N PHE B 109 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG B 118 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 107 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N HIS B 38 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASN B 158 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR B 40 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE B 156 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 156 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 9 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.155A pdb=" N ASN B 61 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 56 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 52 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 53 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 15 removed outlier: 6.302A pdb=" N GLY C 12 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER C 127 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C 14 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET C 36 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER C 52 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 120 removed outlier: 4.481A pdb=" N PHE D 109 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG D 118 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL D 107 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 156 " --> pdb=" O PHE D 9 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE D 9 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 81 through 85 removed outlier: 4.738A pdb=" N ASN D 61 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR D 54 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE D 63 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE D 52 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE D 65 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER D 50 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB6, first strand: chain 'E' and resid 12 through 15 removed outlier: 6.333A pdb=" N GLY E 12 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER E 127 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL E 14 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET E 36 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER E 52 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP E 38 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 12 through 15 removed outlier: 6.333A pdb=" N GLY E 12 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER E 127 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL E 14 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AB9, first strand: chain 'F' and resid 114 through 115 removed outlier: 4.001A pdb=" N ILE F 106 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N HIS F 38 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN F 158 " --> pdb=" O HIS F 38 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR F 40 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE F 156 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY F 154 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE F 156 " --> pdb=" O PHE F 9 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N LYS F 7 " --> pdb=" O ASN F 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 80 through 85 removed outlier: 6.012A pdb=" N ASN F 61 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR F 56 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 52 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP F 67 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N SER F 50 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 5 through 9 Processing sheet with id=AC3, first strand: chain 'G' and resid 12 through 15 removed outlier: 6.314A pdb=" N GLY G 12 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER G 127 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL G 14 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET G 36 " --> pdb=" O SER G 52 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER G 52 " --> pdb=" O MET G 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP G 38 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 114 through 115 Processing sheet with id=AC5, first strand: chain 'H' and resid 114 through 115 removed outlier: 4.063A pdb=" N ILE H 106 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N HIS H 38 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN H 158 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR H 40 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE H 156 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 154 " --> pdb=" O PHE H 11 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE H 156 " --> pdb=" O PHE H 9 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 80 through 85 removed outlier: 5.968A pdb=" N ASN H 61 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR H 56 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE H 52 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP H 67 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER H 50 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AC8, first strand: chain 'I' and resid 12 through 15 removed outlier: 6.185A pdb=" N GLY I 12 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER I 127 " --> pdb=" O GLY I 12 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL I 14 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER I 101 " --> pdb=" O TYR I 35 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR I 35 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET I 36 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER I 52 " --> pdb=" O MET I 36 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP I 38 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 114 through 115 Processing sheet with id=AD1, first strand: chain 'J' and resid 114 through 115 removed outlier: 3.688A pdb=" N ILE J 106 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR J 34 " --> pdb=" O MET J 161 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET J 161 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N CYS J 36 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL J 159 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE J 156 " --> pdb=" O PHE J 9 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN J 158 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N LYS J 7 " --> pdb=" O ASN J 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 80 through 85 removed outlier: 5.988A pdb=" N ASN J 61 " --> pdb=" O THR J 56 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR J 56 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP J 67 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER J 50 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER J 53 " --> pdb=" O ILE J 134 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE J 134 " --> pdb=" O SER J 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA J 55 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE J 133 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AD4, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.219A pdb=" N GLY K 12 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET K 36 " --> pdb=" O SER K 52 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER K 52 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP K 38 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 114 through 115 Processing sheet with id=AD6, first strand: chain 'L' and resid 114 through 115 removed outlier: 3.973A pdb=" N ILE L 106 " --> pdb=" O GLU L 101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR L 34 " --> pdb=" O MET L 161 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET L 161 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS L 36 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL L 159 " --> pdb=" O CYS L 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 156 " --> pdb=" O PHE L 9 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN L 158 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N LYS L 7 " --> pdb=" O ASN L 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 80 through 85 removed outlier: 5.913A pdb=" N ASN L 61 " --> pdb=" O THR L 56 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR L 56 " --> pdb=" O ASN L 61 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP L 67 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER L 50 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER L 53 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE L 134 " --> pdb=" O SER L 53 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE L 133 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AD9, first strand: chain 'M' and resid 12 through 15 removed outlier: 6.199A pdb=" N GLY M 12 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER M 127 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL M 14 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET M 36 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER M 52 " --> pdb=" O MET M 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP M 38 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 114 through 115 Processing sheet with id=AE2, first strand: chain 'N' and resid 114 through 115 removed outlier: 3.678A pdb=" N ILE N 106 " --> pdb=" O GLU N 101 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS N 38 " --> pdb=" O ASN N 158 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN N 158 " --> pdb=" O HIS N 38 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR N 40 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE N 156 " --> pdb=" O TYR N 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY N 154 " --> pdb=" O PHE N 11 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN N 158 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N LYS N 7 " --> pdb=" O ASN N 158 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 80 through 85 removed outlier: 6.000A pdb=" N ASN N 61 " --> pdb=" O THR N 56 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR N 56 " --> pdb=" O ASN N 61 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP N 67 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER N 50 " --> pdb=" O TRP N 67 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER N 53 " --> pdb=" O ILE N 134 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA N 55 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE N 133 " --> pdb=" O LEU N 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 5 through 9 Processing sheet with id=AE5, first strand: chain 'P' and resid 12 through 15 removed outlier: 6.234A pdb=" N GLY P 12 " --> pdb=" O THR P 125 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER P 127 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL P 14 " --> pdb=" O SER P 127 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP P 38 " --> pdb=" O VAL P 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 114 through 115 Processing sheet with id=AE7, first strand: chain 'Q' and resid 114 through 115 removed outlier: 3.793A pdb=" N ILE Q 106 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS Q 38 " --> pdb=" O ASN Q 158 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN Q 158 " --> pdb=" O HIS Q 38 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR Q 40 " --> pdb=" O ILE Q 156 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE Q 156 " --> pdb=" O TYR Q 40 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE Q 156 " --> pdb=" O PHE Q 9 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASN Q 158 " --> pdb=" O LYS Q 7 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N LYS Q 7 " --> pdb=" O ASN Q 158 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 80 through 85 removed outlier: 5.935A pdb=" N ASN Q 61 " --> pdb=" O THR Q 56 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR Q 56 " --> pdb=" O ASN Q 61 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP Q 67 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER Q 50 " --> pdb=" O TRP Q 67 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER Q 53 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE Q 133 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 5 through 9 Processing sheet with id=AF1, first strand: chain 'R' and resid 12 through 15 removed outlier: 6.179A pdb=" N GLY R 12 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N SER R 127 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL R 14 " --> pdb=" O SER R 127 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER R 101 " --> pdb=" O TYR R 35 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR R 35 " --> pdb=" O SER R 101 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET R 36 " --> pdb=" O SER R 52 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER R 52 " --> pdb=" O MET R 36 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP R 38 " --> pdb=" O VAL R 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 12 through 15 removed outlier: 6.179A pdb=" N GLY R 12 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N SER R 127 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL R 14 " --> pdb=" O SER R 127 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 114 through 115 Processing sheet with id=AF4, first strand: chain 'T' and resid 114 through 115 removed outlier: 3.682A pdb=" N ILE T 106 " --> pdb=" O GLU T 101 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR T 34 " --> pdb=" O MET T 161 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET T 161 " --> pdb=" O THR T 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS T 36 " --> pdb=" O VAL T 159 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL T 159 " --> pdb=" O CYS T 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE T 156 " --> pdb=" O PHE T 9 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASN T 158 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 10.497A pdb=" N LYS T 7 " --> pdb=" O ASN T 158 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 80 through 85 removed outlier: 6.006A pdb=" N ASN T 61 " --> pdb=" O THR T 56 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR T 56 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP T 67 " --> pdb=" O SER T 50 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER T 50 " --> pdb=" O TRP T 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER T 53 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA T 55 " --> pdb=" O SER T 132 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE T 133 " --> pdb=" O LEU T 22 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.93 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 15920 1.01 - 1.21: 8 1.21 - 1.41: 11408 1.41 - 1.61: 15244 1.61 - 1.81: 120 Bond restraints: 42700 Sorted by residual: bond pdb=" C THR N 46 " pdb=" N ARG N 47 " ideal model delta sigma weight residual 1.331 1.448 -0.118 1.41e-02 5.03e+03 6.95e+01 bond pdb=" C GLY M 12 " pdb=" N LEU M 13 " ideal model delta sigma weight residual 1.330 1.441 -0.111 1.36e-02 5.41e+03 6.72e+01 bond pdb=" C SER L 53 " pdb=" N TYR L 54 " ideal model delta sigma weight residual 1.330 1.223 0.107 1.32e-02 5.74e+03 6.57e+01 bond pdb=" C ILE D 63 " pdb=" N LEU D 64 " ideal model delta sigma weight residual 1.332 1.440 -0.108 1.35e-02 5.49e+03 6.45e+01 bond pdb=" C ILE B 65 " pdb=" N PHE B 66 " ideal model delta sigma weight residual 1.331 1.228 0.103 1.30e-02 5.92e+03 6.30e+01 ... (remaining 42695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.57: 72396 5.57 - 11.13: 175 11.13 - 16.70: 3 16.70 - 22.26: 0 22.26 - 27.83: 6 Bond angle restraints: 72580 Sorted by residual: angle pdb=" CG2 THR D 46 " pdb=" CB THR D 46 " pdb=" HB THR D 46 " ideal model delta sigma weight residual 108.00 80.17 27.83 3.00e+00 1.11e-01 8.60e+01 angle pdb=" OG1 THR D 46 " pdb=" CB THR D 46 " pdb=" HB THR D 46 " ideal model delta sigma weight residual 109.00 82.32 26.68 3.00e+00 1.11e-01 7.91e+01 angle pdb=" CA THR D 46 " pdb=" CB THR D 46 " pdb=" HB THR D 46 " ideal model delta sigma weight residual 109.00 82.58 26.42 3.00e+00 1.11e-01 7.76e+01 angle pdb=" CG2 THR N 46 " pdb=" CB THR N 46 " pdb=" HB THR N 46 " ideal model delta sigma weight residual 108.00 81.74 26.26 3.00e+00 1.11e-01 7.66e+01 angle pdb=" OG1 THR N 46 " pdb=" CB THR N 46 " pdb=" HB THR N 46 " ideal model delta sigma weight residual 109.00 83.33 25.67 3.00e+00 1.11e-01 7.32e+01 ... (remaining 72575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 19004 17.85 - 35.71: 1776 35.71 - 53.56: 476 53.56 - 71.41: 135 71.41 - 89.26: 40 Dihedral angle restraints: 21431 sinusoidal: 10511 harmonic: 10920 Sorted by residual: dihedral pdb=" C GLU B 81 " pdb=" N GLU B 81 " pdb=" CA GLU B 81 " pdb=" CB GLU B 81 " ideal model delta harmonic sigma weight residual -122.60 -111.24 -11.36 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" CA LEU B 121 " pdb=" C LEU B 121 " pdb=" N LYS B 122 " pdb=" CA LYS B 122 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C SER G 104 " pdb=" N SER G 104 " pdb=" CA SER G 104 " pdb=" CB SER G 104 " ideal model delta harmonic sigma weight residual -122.60 -112.68 -9.92 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 21428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.297: 3895 0.297 - 0.594: 3 0.594 - 0.891: 0 0.891 - 1.188: 0 1.188 - 1.485: 2 Chirality restraints: 3900 Sorted by residual: chirality pdb=" CB THR N 46 " pdb=" CA THR N 46 " pdb=" OG1 THR N 46 " pdb=" CG2 THR N 46 " both_signs ideal model delta sigma weight residual False 2.55 1.07 1.48 2.00e-01 2.50e+01 5.51e+01 chirality pdb=" CB THR D 46 " pdb=" CA THR D 46 " pdb=" OG1 THR D 46 " pdb=" CG2 THR D 46 " both_signs ideal model delta sigma weight residual False 2.55 1.26 1.29 2.00e-01 2.50e+01 4.15e+01 chirality pdb=" CA ASN H 145 " pdb=" N ASN H 145 " pdb=" C ASN H 145 " pdb=" CB ASN H 145 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 ... (remaining 3897 not shown) Planarity restraints: 6600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN S 145 " -0.014 2.00e-02 2.50e+03 4.90e-01 3.60e+03 pdb=" CG ASN S 145 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN S 145 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN S 145 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN S 145 " 0.849 2.00e-02 2.50e+03 pdb="HD22 ASN S 145 " -0.847 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 145 " -0.264 2.00e-02 2.50e+03 4.55e-01 3.10e+03 pdb=" CG ASN N 145 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN N 145 " 0.258 2.00e-02 2.50e+03 pdb=" ND2 ASN N 145 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN N 145 " 0.734 2.00e-02 2.50e+03 pdb="HD22 ASN N 145 " -0.752 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 160 " -0.318 2.00e-02 2.50e+03 4.02e-01 2.42e+03 pdb=" CG ASN J 160 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN J 160 " 0.304 2.00e-02 2.50e+03 pdb=" ND2 ASN J 160 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN J 160 " 0.612 2.00e-02 2.50e+03 pdb="HD22 ASN J 160 " -0.631 2.00e-02 2.50e+03 ... (remaining 6597 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 386 2.02 - 2.67: 47192 2.67 - 3.31: 106330 3.31 - 3.96: 144845 3.96 - 4.60: 216882 Nonbonded interactions: 515635 Sorted by model distance: nonbonded pdb=" HG3 GLU B 14 " pdb="HH22 ARG B 47 " model vdw 1.377 2.270 nonbonded pdb=" OE1 GLU B 130 " pdb=" H GLU B 130 " model vdw 1.462 2.450 nonbonded pdb="HD22 LEU B 37 " pdb="HD11 ILE B 96 " model vdw 1.492 2.440 nonbonded pdb=" HA2 GLY N 136 " pdb=" HG LEU N 152 " model vdw 1.500 2.440 nonbonded pdb=" HA2 GLY L 136 " pdb=" HG LEU L 152 " model vdw 1.515 2.440 ... (remaining 515630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.270 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 42.610 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.657 26797 Z= 0.599 Angle : 1.121 24.275 36364 Z= 0.692 Chirality : 0.064 1.485 3900 Planarity : 0.005 0.073 4660 Dihedral : 14.620 87.604 9600 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 41.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.46 % Allowed : 16.62 % Favored : 82.92 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3270 helix: 1.18 (0.49), residues: 110 sheet: -0.39 (0.15), residues: 1220 loop : -1.69 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 188 TYR 0.030 0.001 TYR T 125 PHE 0.017 0.002 PHE T 39 TRP 0.017 0.001 TRP Q 205 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00615 (26780) covalent geometry : angle 1.06757 (36330) SS BOND : bond 0.34524 ( 17) SS BOND : angle 11.21082 ( 34) hydrogen bonds : bond 0.20018 ( 946) hydrogen bonds : angle 8.13443 ( 2370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 518 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 75 ASP cc_start: 0.7637 (t0) cc_final: 0.7070 (t0) REVERT: O 78 GLU cc_start: 0.9483 (mp0) cc_final: 0.9074 (mp0) REVERT: O 102 GLN cc_start: 0.9043 (tp40) cc_final: 0.8338 (tp-100) REVERT: O 114 GLU cc_start: 0.9515 (mp0) cc_final: 0.9167 (mp0) REVERT: O 115 TYR cc_start: 0.8938 (m-80) cc_final: 0.8444 (m-80) REVERT: A 85 MET cc_start: 0.9255 (mtm) cc_final: 0.8936 (mtm) REVERT: A 125 THR cc_start: 0.9170 (m) cc_final: 0.8879 (p) REVERT: B 58 ARG cc_start: 0.9458 (ttp-110) cc_final: 0.9249 (ttp80) REVERT: C 36 MET cc_start: 0.9385 (mmp) cc_final: 0.9082 (mmm) REVERT: C 75 ASP cc_start: 0.7426 (t0) cc_final: 0.6752 (t0) REVERT: C 78 GLU cc_start: 0.9392 (mp0) cc_final: 0.8961 (mp0) REVERT: C 82 TYR cc_start: 0.9059 (m-80) cc_final: 0.8512 (m-10) REVERT: C 115 TYR cc_start: 0.9097 (m-80) cc_final: 0.8306 (m-80) REVERT: C 125 THR cc_start: 0.9234 (m) cc_final: 0.8967 (p) REVERT: D 18 SER cc_start: 0.9623 (p) cc_final: 0.9370 (m) REVERT: F 197 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8857 (pt0) REVERT: G 101 SER cc_start: 0.7883 (t) cc_final: 0.7315 (p) REVERT: G 114 GLU cc_start: 0.9475 (mp0) cc_final: 0.9131 (mp0) REVERT: G 125 THR cc_start: 0.9118 (m) cc_final: 0.8779 (p) REVERT: H 73 TYR cc_start: 0.9361 (m-80) cc_final: 0.9099 (m-80) REVERT: H 197 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8775 (pt0) REVERT: I 6 LEU cc_start: 0.8350 (mm) cc_final: 0.7765 (mm) REVERT: I 21 ARG cc_start: 0.9373 (ttt90) cc_final: 0.9161 (tpt170) REVERT: I 46 GLU cc_start: 0.9007 (pm20) cc_final: 0.8738 (pm20) REVERT: I 48 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9034 (mp0) REVERT: I 62 TYR cc_start: 0.6998 (m-80) cc_final: 0.5752 (m-80) REVERT: K 46 GLU cc_start: 0.8863 (pm20) cc_final: 0.8603 (pm20) REVERT: K 47 ARG cc_start: 0.9020 (mtt90) cc_final: 0.8757 (mmt90) REVERT: K 48 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8265 (mp0) REVERT: K 75 ASP cc_start: 0.6842 (p0) cc_final: 0.5931 (p0) REVERT: K 125 THR cc_start: 0.9286 (m) cc_final: 0.9075 (p) REVERT: M 47 ARG cc_start: 0.8903 (mtt90) cc_final: 0.8693 (mmt90) REVERT: M 85 MET cc_start: 0.8719 (mtm) cc_final: 0.8475 (mpp) REVERT: M 86 ASN cc_start: 0.8198 (m-40) cc_final: 0.7957 (m-40) REVERT: M 122 THR cc_start: 0.8993 (t) cc_final: 0.8567 (p) REVERT: P 48 GLU cc_start: 0.8542 (mp0) cc_final: 0.8137 (mp0) REVERT: P 71 THR cc_start: 0.8578 (m) cc_final: 0.8192 (p) REVERT: R 21 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8501 (ttp80) REVERT: R 48 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8600 (mp0) REVERT: R 97 TYR cc_start: 0.7856 (m-80) cc_final: 0.7328 (m-80) REVERT: R 120 GLN cc_start: 0.7379 (pm20) cc_final: 0.7153 (pm20) REVERT: R 122 THR cc_start: 0.8538 (t) cc_final: 0.8042 (p) REVERT: T 161 MET cc_start: 0.8225 (ttt) cc_final: 0.7836 (tpp) outliers start: 13 outliers final: 11 residues processed: 526 average time/residue: 0.3755 time to fit residues: 297.9778 Evaluate side-chains 417 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 406 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain R residue 7 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 10.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 55 GLN O 59 ASN ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 95 HIS S 139 GLN A 34 HIS A 59 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 95 HIS B 150 GLN C 59 ASN C 87 ASN D 150 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN F 139 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN H 145 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** N 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 ASN Q 139 GLN Q 160 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055369 restraints weight = 232842.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057555 restraints weight = 85210.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058820 restraints weight = 43464.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059578 restraints weight = 27302.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059909 restraints weight = 19818.622| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26797 Z= 0.203 Angle : 0.604 11.071 36364 Z= 0.328 Chirality : 0.054 1.395 3900 Planarity : 0.004 0.044 4660 Dihedral : 4.822 45.353 3634 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 30.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.57 % Allowed : 17.11 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 3270 helix: -0.31 (0.44), residues: 170 sheet: -0.57 (0.15), residues: 1190 loop : -1.31 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 58 TYR 0.023 0.002 TYR F 54 PHE 0.016 0.001 PHE O 31 TRP 0.011 0.001 TRP B 67 HIS 0.007 0.001 HIS S 38 Details of bonding type rmsd covalent geometry : bond 0.00444 (26780) covalent geometry : angle 0.60330 (36330) SS BOND : bond 0.00413 ( 17) SS BOND : angle 0.87767 ( 34) hydrogen bonds : bond 0.04582 ( 946) hydrogen bonds : angle 5.85633 ( 2370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 429 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 ARG cc_start: 0.9232 (mmt90) cc_final: 0.8987 (mmt90) REVERT: O 75 ASP cc_start: 0.7737 (t0) cc_final: 0.6178 (t0) REVERT: O 78 GLU cc_start: 0.9444 (mp0) cc_final: 0.8852 (mp0) REVERT: O 114 GLU cc_start: 0.9388 (mp0) cc_final: 0.9143 (mp0) REVERT: A 78 GLU cc_start: 0.9306 (mp0) cc_final: 0.8914 (mp0) REVERT: A 92 ASP cc_start: 0.9149 (m-30) cc_final: 0.8912 (m-30) REVERT: A 106 TYR cc_start: 0.8490 (m-10) cc_final: 0.8202 (m-10) REVERT: A 125 THR cc_start: 0.9330 (m) cc_final: 0.8944 (p) REVERT: C 33 ARG cc_start: 0.9343 (mmt90) cc_final: 0.8774 (mmt90) REVERT: C 75 ASP cc_start: 0.7857 (t0) cc_final: 0.7628 (t0) REVERT: C 82 TYR cc_start: 0.9093 (m-80) cc_final: 0.8560 (m-10) REVERT: E 78 GLU cc_start: 0.9423 (mp0) cc_final: 0.8851 (mp0) REVERT: E 106 TYR cc_start: 0.8343 (m-10) cc_final: 0.7808 (m-10) REVERT: G 53 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9048 (tt) REVERT: G 82 TYR cc_start: 0.8997 (m-80) cc_final: 0.8746 (m-10) REVERT: G 114 GLU cc_start: 0.9223 (mp0) cc_final: 0.9020 (mp0) REVERT: I 21 ARG cc_start: 0.9386 (ttt90) cc_final: 0.9128 (tpt170) REVERT: I 48 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9093 (mp0) REVERT: I 62 TYR cc_start: 0.7949 (m-80) cc_final: 0.6995 (m-80) REVERT: I 69 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.8069 (ttp-110) REVERT: I 87 ASN cc_start: 0.9539 (m110) cc_final: 0.9258 (t0) REVERT: I 106 TYR cc_start: 0.8224 (m-80) cc_final: 0.7948 (m-80) REVERT: K 21 ARG cc_start: 0.9281 (tpt-90) cc_final: 0.8964 (ttt90) REVERT: K 62 TYR cc_start: 0.7111 (m-80) cc_final: 0.6867 (m-80) REVERT: M 36 MET cc_start: 0.7803 (mmm) cc_final: 0.7355 (mmm) REVERT: M 47 ARG cc_start: 0.8787 (mtt90) cc_final: 0.8543 (mmt90) REVERT: M 85 MET cc_start: 0.8961 (mtm) cc_final: 0.8756 (mpp) REVERT: M 96 TYR cc_start: 0.8377 (m-10) cc_final: 0.8143 (m-10) REVERT: M 122 THR cc_start: 0.9034 (t) cc_final: 0.8559 (p) REVERT: P 85 MET cc_start: 0.8639 (mpp) cc_final: 0.8416 (mpp) REVERT: R 21 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8478 (tpp80) REVERT: R 97 TYR cc_start: 0.7708 (m-80) cc_final: 0.7439 (m-80) REVERT: R 122 THR cc_start: 0.8997 (t) cc_final: 0.8446 (p) outliers start: 73 outliers final: 53 residues processed: 466 average time/residue: 0.3673 time to fit residues: 255.4929 Evaluate side-chains 454 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 400 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain S residue 70 ASP Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 98 CYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 97 TYR Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain T residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 161 optimal weight: 50.0000 chunk 144 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN F 195 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 ASN P 76 ASN R 59 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053715 restraints weight = 233271.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.055924 restraints weight = 83315.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057205 restraints weight = 42297.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.057781 restraints weight = 26364.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058271 restraints weight = 19746.637| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26797 Z= 0.225 Angle : 0.574 11.350 36364 Z= 0.315 Chirality : 0.053 1.383 3900 Planarity : 0.004 0.039 4660 Dihedral : 4.469 43.407 3614 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.06 % Allowed : 17.11 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3270 helix: -0.07 (0.43), residues: 170 sheet: -0.52 (0.14), residues: 1320 loop : -1.53 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 58 TYR 0.023 0.001 TYR R 105 PHE 0.013 0.001 PHE D 52 TRP 0.009 0.001 TRP J 67 HIS 0.008 0.001 HIS S 38 Details of bonding type rmsd covalent geometry : bond 0.00480 (26780) covalent geometry : angle 0.57361 (36330) SS BOND : bond 0.00304 ( 17) SS BOND : angle 0.83375 ( 34) hydrogen bonds : bond 0.04394 ( 946) hydrogen bonds : angle 5.48626 ( 2370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 404 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 ARG cc_start: 0.9214 (mmt90) cc_final: 0.8994 (mmt90) REVERT: O 36 MET cc_start: 0.8987 (mmm) cc_final: 0.8568 (mmm) REVERT: O 106 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: O 114 GLU cc_start: 0.9320 (mp0) cc_final: 0.8900 (mp0) REVERT: A 78 GLU cc_start: 0.9371 (mp0) cc_final: 0.8923 (mp0) REVERT: A 106 TYR cc_start: 0.8645 (m-10) cc_final: 0.8308 (m-10) REVERT: A 125 THR cc_start: 0.9288 (m) cc_final: 0.8917 (p) REVERT: C 33 ARG cc_start: 0.9347 (mmt90) cc_final: 0.8769 (mmt90) REVERT: C 36 MET cc_start: 0.9447 (mmp) cc_final: 0.9075 (mmm) REVERT: C 106 TYR cc_start: 0.8114 (m-10) cc_final: 0.7823 (m-10) REVERT: D 4 MET cc_start: 0.9087 (mmm) cc_final: 0.8732 (mmm) REVERT: E 78 GLU cc_start: 0.9389 (mp0) cc_final: 0.8913 (mp0) REVERT: E 106 TYR cc_start: 0.8625 (m-10) cc_final: 0.7954 (m-10) REVERT: G 78 GLU cc_start: 0.9471 (mp0) cc_final: 0.8951 (mp0) REVERT: G 82 TYR cc_start: 0.9069 (m-80) cc_final: 0.8810 (m-10) REVERT: G 106 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: G 114 GLU cc_start: 0.9146 (mp0) cc_final: 0.8705 (mp0) REVERT: I 62 TYR cc_start: 0.7902 (m-80) cc_final: 0.7239 (m-80) REVERT: I 106 TYR cc_start: 0.8393 (m-80) cc_final: 0.8070 (m-80) REVERT: K 21 ARG cc_start: 0.9127 (tpt-90) cc_final: 0.8873 (ttt90) REVERT: K 36 MET cc_start: 0.7980 (mmm) cc_final: 0.7718 (mmm) REVERT: K 62 TYR cc_start: 0.7237 (m-80) cc_final: 0.6816 (m-80) REVERT: M 36 MET cc_start: 0.7734 (mmm) cc_final: 0.7491 (mmm) REVERT: M 62 TYR cc_start: 0.7202 (m-80) cc_final: 0.6378 (m-80) REVERT: P 62 TYR cc_start: 0.7488 (m-80) cc_final: 0.7177 (m-80) REVERT: P 72 ILE cc_start: 0.7898 (tt) cc_final: 0.7564 (tt) REVERT: P 85 MET cc_start: 0.8593 (mpp) cc_final: 0.8305 (mpp) REVERT: R 8 GLU cc_start: 0.6757 (pm20) cc_final: 0.6157 (pm20) REVERT: R 21 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8393 (tpp80) REVERT: R 97 TYR cc_start: 0.7680 (m-80) cc_final: 0.7343 (m-80) REVERT: R 122 THR cc_start: 0.8876 (t) cc_final: 0.8382 (p) outliers start: 87 outliers final: 71 residues processed: 442 average time/residue: 0.3580 time to fit residues: 234.8051 Evaluate side-chains 458 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 385 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain O residue 55 GLN Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain S residue 70 ASP Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 98 CYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 19 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 139 optimal weight: 0.0170 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 38 HIS A 34 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN M 59 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054903 restraints weight = 230205.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.057192 restraints weight = 80396.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058514 restraints weight = 39924.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.059231 restraints weight = 24834.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059557 restraints weight = 18113.193| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26797 Z= 0.105 Angle : 0.513 11.280 36364 Z= 0.278 Chirality : 0.053 1.390 3900 Planarity : 0.003 0.038 4660 Dihedral : 4.196 44.884 3613 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.83 % Allowed : 19.12 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3270 helix: 0.39 (0.44), residues: 170 sheet: -0.37 (0.14), residues: 1300 loop : -1.29 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 47 TYR 0.019 0.001 TYR S 125 PHE 0.011 0.001 PHE D 52 TRP 0.008 0.001 TRP B 67 HIS 0.007 0.001 HIS S 38 Details of bonding type rmsd covalent geometry : bond 0.00235 (26780) covalent geometry : angle 0.51297 (36330) SS BOND : bond 0.00114 ( 17) SS BOND : angle 0.33679 ( 34) hydrogen bonds : bond 0.03580 ( 946) hydrogen bonds : angle 5.18397 ( 2370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 422 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 78 GLU cc_start: 0.9490 (mp0) cc_final: 0.8925 (mp0) REVERT: O 106 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: O 114 GLU cc_start: 0.9406 (mp0) cc_final: 0.8994 (mp0) REVERT: A 78 GLU cc_start: 0.9414 (mp0) cc_final: 0.8943 (mp0) REVERT: A 106 TYR cc_start: 0.8552 (m-10) cc_final: 0.8206 (m-10) REVERT: A 125 THR cc_start: 0.9304 (m) cc_final: 0.8942 (p) REVERT: B 14 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 33 ARG cc_start: 0.9363 (mmt90) cc_final: 0.8791 (mmt90) REVERT: C 36 MET cc_start: 0.9461 (mmp) cc_final: 0.8930 (mmm) REVERT: C 82 TYR cc_start: 0.8973 (m-80) cc_final: 0.8722 (m-10) REVERT: C 106 TYR cc_start: 0.8268 (m-10) cc_final: 0.7788 (m-10) REVERT: D 4 MET cc_start: 0.8977 (mmm) cc_final: 0.8610 (mmm) REVERT: E 33 ARG cc_start: 0.9253 (mmt90) cc_final: 0.9042 (mmt90) REVERT: E 78 GLU cc_start: 0.9444 (mp0) cc_final: 0.8925 (mp0) REVERT: E 106 TYR cc_start: 0.8423 (m-10) cc_final: 0.7655 (m-10) REVERT: G 75 ASP cc_start: 0.7756 (t0) cc_final: 0.6437 (t0) REVERT: G 78 GLU cc_start: 0.9470 (mp0) cc_final: 0.8886 (mp0) REVERT: G 82 TYR cc_start: 0.9025 (m-80) cc_final: 0.8757 (m-10) REVERT: G 106 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: G 114 GLU cc_start: 0.9245 (mp0) cc_final: 0.9000 (mp0) REVERT: H 125 TYR cc_start: 0.8561 (t80) cc_final: 0.8080 (t80) REVERT: I 6 LEU cc_start: 0.8334 (mm) cc_final: 0.7890 (mm) REVERT: I 36 MET cc_start: 0.7755 (mmm) cc_final: 0.7315 (mmm) REVERT: I 62 TYR cc_start: 0.7890 (m-80) cc_final: 0.6921 (m-80) REVERT: I 69 ARG cc_start: 0.7863 (ttp-110) cc_final: 0.7520 (ttp80) REVERT: I 106 TYR cc_start: 0.8297 (m-80) cc_final: 0.8010 (m-80) REVERT: I 120 GLN cc_start: 0.7421 (pm20) cc_final: 0.6991 (pm20) REVERT: K 36 MET cc_start: 0.7984 (mmm) cc_final: 0.7731 (mmm) REVERT: K 47 ARG cc_start: 0.8979 (mpp80) cc_final: 0.8481 (mmt90) REVERT: K 62 TYR cc_start: 0.7200 (m-80) cc_final: 0.6974 (m-80) REVERT: K 69 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.8315 (ttp-110) REVERT: K 85 MET cc_start: 0.8259 (mpp) cc_final: 0.7763 (mpp) REVERT: K 87 ASN cc_start: 0.9629 (m110) cc_final: 0.9262 (t0) REVERT: M 47 ARG cc_start: 0.8708 (mpp80) cc_final: 0.8144 (mmt90) REVERT: M 62 TYR cc_start: 0.7165 (m-80) cc_final: 0.6325 (m-80) REVERT: M 85 MET cc_start: 0.8506 (mpp) cc_final: 0.8247 (mpp) REVERT: P 62 TYR cc_start: 0.7420 (m-80) cc_final: 0.7157 (m-80) REVERT: P 72 ILE cc_start: 0.7815 (tt) cc_final: 0.7455 (tt) REVERT: P 85 MET cc_start: 0.8717 (mpp) cc_final: 0.8242 (mpp) REVERT: R 21 ARG cc_start: 0.8775 (tpp80) cc_final: 0.8412 (tpp80) REVERT: R 87 ASN cc_start: 0.9676 (m110) cc_final: 0.9296 (t0) REVERT: R 120 GLN cc_start: 0.7378 (pm20) cc_final: 0.7147 (pm20) REVERT: R 122 THR cc_start: 0.8961 (t) cc_final: 0.8511 (p) outliers start: 52 outliers final: 42 residues processed: 446 average time/residue: 0.3488 time to fit residues: 230.6344 Evaluate side-chains 453 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 409 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 230 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 181 optimal weight: 0.0980 chunk 152 optimal weight: 6.9990 chunk 257 optimal weight: 40.0000 chunk 273 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 250 optimal weight: 30.0000 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 61 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.080586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.052804 restraints weight = 231220.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055040 restraints weight = 80745.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056214 restraints weight = 40655.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057014 restraints weight = 25960.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057432 restraints weight = 18824.670| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26797 Z= 0.177 Angle : 0.533 11.350 36364 Z= 0.289 Chirality : 0.053 1.386 3900 Planarity : 0.003 0.035 4660 Dihedral : 4.232 48.882 3613 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.78 % Allowed : 18.84 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3270 helix: 0.39 (0.44), residues: 170 sheet: -0.56 (0.14), residues: 1330 loop : -1.27 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 69 TYR 0.021 0.001 TYR S 125 PHE 0.017 0.001 PHE O 31 TRP 0.008 0.001 TRP T 67 HIS 0.005 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00385 (26780) covalent geometry : angle 0.53334 (36330) SS BOND : bond 0.00213 ( 17) SS BOND : angle 0.51992 ( 34) hydrogen bonds : bond 0.03744 ( 946) hydrogen bonds : angle 5.13551 ( 2370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 405 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 36 MET cc_start: 0.9014 (mmm) cc_final: 0.8509 (mmm) REVERT: O 78 GLU cc_start: 0.9478 (mp0) cc_final: 0.8900 (mp0) REVERT: O 106 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: O 114 GLU cc_start: 0.9369 (mp0) cc_final: 0.9129 (mp0) REVERT: O 125 THR cc_start: 0.9476 (m) cc_final: 0.8984 (p) REVERT: A 78 GLU cc_start: 0.9394 (mp0) cc_final: 0.8880 (mp0) REVERT: A 106 TYR cc_start: 0.8652 (m-10) cc_final: 0.8244 (m-10) REVERT: C 33 ARG cc_start: 0.9346 (mmt90) cc_final: 0.8759 (mmt90) REVERT: C 36 MET cc_start: 0.9456 (mmp) cc_final: 0.8895 (mmm) REVERT: C 82 TYR cc_start: 0.9041 (m-80) cc_final: 0.8721 (m-10) REVERT: C 106 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: E 78 GLU cc_start: 0.9415 (mp0) cc_final: 0.8886 (mp0) REVERT: E 106 TYR cc_start: 0.8594 (m-10) cc_final: 0.7840 (m-10) REVERT: G 78 GLU cc_start: 0.9463 (mp0) cc_final: 0.8881 (mp0) REVERT: G 106 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (m-10) REVERT: G 114 GLU cc_start: 0.9171 (mp0) cc_final: 0.8880 (mp0) REVERT: I 6 LEU cc_start: 0.8448 (mm) cc_final: 0.7957 (mm) REVERT: I 36 MET cc_start: 0.7853 (mmm) cc_final: 0.7420 (mmm) REVERT: I 62 TYR cc_start: 0.7895 (m-80) cc_final: 0.6958 (m-80) REVERT: I 69 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7564 (ttp80) REVERT: I 106 TYR cc_start: 0.8354 (m-80) cc_final: 0.8004 (m-80) REVERT: K 36 MET cc_start: 0.7994 (mmm) cc_final: 0.7606 (mmm) REVERT: K 62 TYR cc_start: 0.7303 (m-80) cc_final: 0.6979 (m-80) REVERT: K 76 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8968 (m110) REVERT: K 85 MET cc_start: 0.8395 (mpp) cc_final: 0.7734 (mpp) REVERT: K 87 ASN cc_start: 0.9544 (m110) cc_final: 0.9267 (t0) REVERT: M 36 MET cc_start: 0.7921 (mmm) cc_final: 0.7683 (mmm) REVERT: M 62 TYR cc_start: 0.7171 (m-80) cc_final: 0.6403 (m-80) REVERT: M 85 MET cc_start: 0.8547 (mpp) cc_final: 0.7936 (mpp) REVERT: P 62 TYR cc_start: 0.7480 (m-80) cc_final: 0.7123 (m-80) REVERT: P 72 ILE cc_start: 0.7894 (tt) cc_final: 0.7536 (tt) REVERT: P 85 MET cc_start: 0.8739 (mpp) cc_final: 0.8274 (mpp) REVERT: R 8 GLU cc_start: 0.6328 (pm20) cc_final: 0.6070 (pm20) REVERT: R 21 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8380 (tpp80) REVERT: R 87 ASN cc_start: 0.9579 (m110) cc_final: 0.9313 (t0) REVERT: R 122 THR cc_start: 0.8968 (t) cc_final: 0.8497 (p) outliers start: 79 outliers final: 69 residues processed: 439 average time/residue: 0.3584 time to fit residues: 234.3145 Evaluate side-chains 461 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 388 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 55 GLN Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 98 CYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 161 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 102 GLN Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 163 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 198 optimal weight: 40.0000 chunk 209 optimal weight: 20.0000 chunk 197 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 224 optimal weight: 50.0000 chunk 55 optimal weight: 3.9990 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 HIS ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053196 restraints weight = 232964.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055376 restraints weight = 83053.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056623 restraints weight = 42486.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.057191 restraints weight = 26615.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057650 restraints weight = 19997.767| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26797 Z= 0.197 Angle : 0.543 11.274 36364 Z= 0.295 Chirality : 0.052 1.366 3900 Planarity : 0.003 0.064 4660 Dihedral : 4.303 53.226 3613 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.38 % Allowed : 19.12 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3270 helix: 0.39 (0.43), residues: 170 sheet: -0.53 (0.14), residues: 1310 loop : -1.33 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 58 TYR 0.031 0.001 TYR M 82 PHE 0.010 0.001 PHE T 66 TRP 0.009 0.001 TRP T 67 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00424 (26780) covalent geometry : angle 0.54352 (36330) SS BOND : bond 0.00234 ( 17) SS BOND : angle 0.51994 ( 34) hydrogen bonds : bond 0.03755 ( 946) hydrogen bonds : angle 5.09173 ( 2370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 386 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 36 MET cc_start: 0.9004 (mmm) cc_final: 0.8473 (mmm) REVERT: O 78 GLU cc_start: 0.9477 (mp0) cc_final: 0.8906 (mp0) REVERT: O 106 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8311 (m-10) REVERT: O 114 GLU cc_start: 0.9326 (mp0) cc_final: 0.9061 (mp0) REVERT: O 125 THR cc_start: 0.9495 (m) cc_final: 0.8999 (p) REVERT: A 78 GLU cc_start: 0.9411 (mp0) cc_final: 0.8884 (mp0) REVERT: A 106 TYR cc_start: 0.8716 (m-10) cc_final: 0.8298 (m-10) REVERT: C 33 ARG cc_start: 0.9337 (mmt90) cc_final: 0.8772 (mmt90) REVERT: C 36 MET cc_start: 0.9387 (mmp) cc_final: 0.8777 (mmm) REVERT: C 82 TYR cc_start: 0.9086 (m-80) cc_final: 0.8691 (m-10) REVERT: C 102 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7862 (tp-100) REVERT: C 106 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7825 (m-10) REVERT: E 78 GLU cc_start: 0.9427 (mp0) cc_final: 0.8892 (mp0) REVERT: E 106 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7877 (m-10) REVERT: G 36 MET cc_start: 0.8720 (mmm) cc_final: 0.8276 (mmm) REVERT: G 78 GLU cc_start: 0.9473 (mp0) cc_final: 0.8871 (mp0) REVERT: G 114 GLU cc_start: 0.9161 (mp0) cc_final: 0.8860 (mp0) REVERT: I 36 MET cc_start: 0.7932 (mmm) cc_final: 0.7634 (mmm) REVERT: I 62 TYR cc_start: 0.7845 (m-80) cc_final: 0.6909 (m-80) REVERT: I 69 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7795 (ttp-110) REVERT: I 85 MET cc_start: 0.9152 (mtm) cc_final: 0.8798 (mtm) REVERT: I 106 TYR cc_start: 0.8422 (m-80) cc_final: 0.8059 (m-80) REVERT: K 36 MET cc_start: 0.7908 (mmm) cc_final: 0.7481 (mmm) REVERT: K 62 TYR cc_start: 0.7309 (m-80) cc_final: 0.6874 (m-80) REVERT: K 85 MET cc_start: 0.8455 (mpp) cc_final: 0.7783 (mpp) REVERT: K 87 ASN cc_start: 0.9536 (m110) cc_final: 0.9248 (t0) REVERT: K 108 LYS cc_start: 0.2975 (OUTLIER) cc_final: 0.2341 (mmtm) REVERT: M 62 TYR cc_start: 0.7177 (m-80) cc_final: 0.6437 (m-80) REVERT: M 85 MET cc_start: 0.8616 (mpp) cc_final: 0.7922 (mpp) REVERT: P 62 TYR cc_start: 0.7487 (m-80) cc_final: 0.7073 (m-80) REVERT: P 72 ILE cc_start: 0.7895 (tt) cc_final: 0.7544 (tt) REVERT: P 85 MET cc_start: 0.8718 (mpp) cc_final: 0.8248 (mpp) REVERT: R 21 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8416 (tpp80) REVERT: R 76 ASN cc_start: 0.9563 (p0) cc_final: 0.9257 (m-40) REVERT: R 87 ASN cc_start: 0.9579 (m110) cc_final: 0.9298 (t0) REVERT: R 96 TYR cc_start: 0.8355 (m-10) cc_final: 0.8137 (m-10) REVERT: R 122 THR cc_start: 0.8933 (t) cc_final: 0.8438 (p) outliers start: 96 outliers final: 79 residues processed: 430 average time/residue: 0.4050 time to fit residues: 259.2110 Evaluate side-chains 466 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 383 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 55 GLN Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 98 CYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 161 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 17 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 209 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 318 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 chunk 193 optimal weight: 20.0000 chunk 287 optimal weight: 30.0000 chunk 257 optimal weight: 30.0000 chunk 243 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 overall best weight: 12.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN P 59 ASN P 76 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.078487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.050809 restraints weight = 238290.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.052893 restraints weight = 86174.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054108 restraints weight = 44257.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054645 restraints weight = 28227.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055063 restraints weight = 21451.777| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 26797 Z= 0.408 Angle : 0.703 11.778 36364 Z= 0.382 Chirality : 0.054 1.381 3900 Planarity : 0.004 0.043 4660 Dihedral : 5.023 59.638 3613 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 40.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.87 % Allowed : 19.96 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.14), residues: 3270 helix: -0.29 (0.40), residues: 170 sheet: -0.96 (0.14), residues: 1330 loop : -1.70 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 21 TYR 0.037 0.002 TYR C 105 PHE 0.013 0.002 PHE T 66 TRP 0.015 0.002 TRP T 67 HIS 0.008 0.002 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00878 (26780) covalent geometry : angle 0.70299 (36330) SS BOND : bond 0.00533 ( 17) SS BOND : angle 1.02819 ( 34) hydrogen bonds : bond 0.04614 ( 946) hydrogen bonds : angle 5.45161 ( 2370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 356 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 36 MET cc_start: 0.8957 (mmm) cc_final: 0.8626 (mmm) REVERT: O 78 GLU cc_start: 0.9437 (mp0) cc_final: 0.8869 (mp0) REVERT: O 102 GLN cc_start: 0.8663 (tp40) cc_final: 0.8163 (tp40) REVERT: O 106 TYR cc_start: 0.9014 (m-10) cc_final: 0.8708 (m-10) REVERT: O 114 GLU cc_start: 0.9251 (mp0) cc_final: 0.8945 (mp0) REVERT: A 78 GLU cc_start: 0.9386 (mp0) cc_final: 0.8878 (mp0) REVERT: A 106 TYR cc_start: 0.8885 (m-10) cc_final: 0.8574 (m-10) REVERT: C 33 ARG cc_start: 0.9313 (mmt90) cc_final: 0.9017 (mmt90) REVERT: C 36 MET cc_start: 0.9294 (mmp) cc_final: 0.8683 (mmm) REVERT: C 78 GLU cc_start: 0.9411 (mp0) cc_final: 0.8857 (mp0) REVERT: C 82 TYR cc_start: 0.9085 (m-80) cc_final: 0.8701 (m-10) REVERT: C 106 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: E 78 GLU cc_start: 0.9402 (mp0) cc_final: 0.8866 (mp0) REVERT: E 106 TYR cc_start: 0.8997 (m-10) cc_final: 0.8284 (m-10) REVERT: G 36 MET cc_start: 0.8510 (mmm) cc_final: 0.8136 (mmm) REVERT: G 78 GLU cc_start: 0.9461 (mp0) cc_final: 0.8877 (mp0) REVERT: G 106 TYR cc_start: 0.8878 (m-10) cc_final: 0.8664 (m-80) REVERT: G 114 GLU cc_start: 0.9068 (mp0) cc_final: 0.8779 (mp0) REVERT: I 36 MET cc_start: 0.7919 (mmm) cc_final: 0.7597 (mmm) REVERT: I 69 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7713 (ttp80) REVERT: I 85 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8826 (mtm) REVERT: I 106 TYR cc_start: 0.8727 (m-80) cc_final: 0.8415 (m-80) REVERT: K 46 GLU cc_start: 0.8704 (pm20) cc_final: 0.8396 (pm20) REVERT: K 85 MET cc_start: 0.8446 (mpp) cc_final: 0.7985 (mpp) REVERT: K 87 ASN cc_start: 0.9547 (m110) cc_final: 0.9263 (t0) REVERT: K 108 LYS cc_start: 0.3562 (OUTLIER) cc_final: 0.3110 (mmtm) REVERT: M 85 MET cc_start: 0.8487 (mpp) cc_final: 0.7947 (mpp) REVERT: M 89 LYS cc_start: 0.8635 (mppt) cc_final: 0.8406 (mppt) REVERT: P 72 ILE cc_start: 0.8026 (tt) cc_final: 0.7776 (tt) REVERT: P 85 MET cc_start: 0.8716 (mpp) cc_final: 0.8296 (mpp) REVERT: Q 4 MET cc_start: 0.8627 (mmm) cc_final: 0.8427 (mmm) REVERT: R 8 GLU cc_start: 0.6012 (pm20) cc_final: 0.5709 (pm20) REVERT: R 21 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8387 (tpp80) REVERT: R 32 ASN cc_start: 0.8133 (p0) cc_final: 0.7662 (p0) REVERT: R 87 ASN cc_start: 0.9604 (m110) cc_final: 0.9307 (t0) REVERT: R 122 THR cc_start: 0.8743 (t) cc_final: 0.8200 (p) outliers start: 110 outliers final: 98 residues processed: 410 average time/residue: 0.3911 time to fit residues: 239.0120 Evaluate side-chains 451 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 350 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 55 GLN Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 70 ASP Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 98 CYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 161 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 97 TYR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain T residue 190 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 68 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.053362 restraints weight = 232186.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055566 restraints weight = 82270.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056828 restraints weight = 41710.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057516 restraints weight = 26248.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.057830 restraints weight = 19376.900| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26797 Z= 0.111 Angle : 0.544 11.160 36364 Z= 0.295 Chirality : 0.053 1.368 3900 Planarity : 0.003 0.064 4660 Dihedral : 4.460 59.567 3613 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 28.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.32 % Allowed : 21.34 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3270 helix: 0.43 (0.44), residues: 170 sheet: -0.71 (0.14), residues: 1310 loop : -1.33 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 21 TYR 0.020 0.001 TYR R 105 PHE 0.011 0.001 PHE T 66 TRP 0.010 0.001 TRP F 110 HIS 0.007 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00249 (26780) covalent geometry : angle 0.54412 (36330) SS BOND : bond 0.00130 ( 17) SS BOND : angle 0.35509 ( 34) hydrogen bonds : bond 0.03520 ( 946) hydrogen bonds : angle 5.08032 ( 2370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 393 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 78 GLU cc_start: 0.9491 (mp0) cc_final: 0.8938 (mp0) REVERT: O 106 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8560 (m-10) REVERT: O 114 GLU cc_start: 0.9412 (mp0) cc_final: 0.9141 (mp0) REVERT: A 78 GLU cc_start: 0.9453 (mp0) cc_final: 0.8921 (mp0) REVERT: A 106 TYR cc_start: 0.8700 (m-10) cc_final: 0.8307 (m-10) REVERT: A 125 THR cc_start: 0.9329 (m) cc_final: 0.9015 (p) REVERT: C 33 ARG cc_start: 0.9366 (mmt90) cc_final: 0.8814 (mmt90) REVERT: C 36 MET cc_start: 0.9381 (mmp) cc_final: 0.8809 (mmm) REVERT: C 82 TYR cc_start: 0.9063 (m-80) cc_final: 0.8686 (m-10) REVERT: C 106 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: E 78 GLU cc_start: 0.9432 (mp0) cc_final: 0.8911 (mp0) REVERT: E 106 TYR cc_start: 0.8758 (m-10) cc_final: 0.8052 (m-10) REVERT: F 16 ASP cc_start: 0.9154 (p0) cc_final: 0.8382 (t0) REVERT: G 78 GLU cc_start: 0.9517 (mp0) cc_final: 0.8934 (mp0) REVERT: G 114 GLU cc_start: 0.9263 (mp0) cc_final: 0.9016 (mp0) REVERT: H 16 ASP cc_start: 0.9043 (p0) cc_final: 0.8268 (t0) REVERT: I 36 MET cc_start: 0.7924 (mmm) cc_final: 0.7653 (mmm) REVERT: I 62 TYR cc_start: 0.7843 (m-80) cc_final: 0.7169 (m-80) REVERT: I 106 TYR cc_start: 0.8474 (m-80) cc_final: 0.8174 (m-80) REVERT: K 36 MET cc_start: 0.7907 (mmm) cc_final: 0.7453 (mmm) REVERT: K 62 TYR cc_start: 0.7253 (m-80) cc_final: 0.6716 (m-80) REVERT: K 85 MET cc_start: 0.8538 (mpp) cc_final: 0.7909 (mpp) REVERT: K 87 ASN cc_start: 0.9536 (m110) cc_final: 0.9252 (t0) REVERT: K 106 TYR cc_start: 0.8675 (m-80) cc_final: 0.8404 (m-80) REVERT: K 108 LYS cc_start: 0.3195 (OUTLIER) cc_final: 0.2767 (mmtm) REVERT: K 125 THR cc_start: 0.9335 (m) cc_final: 0.9117 (p) REVERT: M 83 LEU cc_start: 0.7932 (tp) cc_final: 0.7505 (tp) REVERT: M 85 MET cc_start: 0.8556 (mpp) cc_final: 0.7996 (mpp) REVERT: P 62 TYR cc_start: 0.7465 (m-80) cc_final: 0.7075 (m-80) REVERT: P 72 ILE cc_start: 0.7905 (tt) cc_final: 0.7528 (tt) REVERT: P 85 MET cc_start: 0.8733 (mpp) cc_final: 0.8254 (mpp) REVERT: R 21 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8426 (tpp80) REVERT: R 85 MET cc_start: 0.8920 (mtm) cc_final: 0.8641 (mtm) REVERT: R 87 ASN cc_start: 0.9600 (m110) cc_final: 0.9311 (t0) REVERT: R 122 THR cc_start: 0.8883 (t) cc_final: 0.8472 (p) outliers start: 66 outliers final: 60 residues processed: 423 average time/residue: 0.3887 time to fit residues: 245.0870 Evaluate side-chains 447 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 384 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 161 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 244 optimal weight: 20.0000 chunk 250 optimal weight: 30.0000 chunk 228 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 253 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 192 optimal weight: 50.0000 chunk 274 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.079870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.052379 restraints weight = 235391.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.054530 restraints weight = 84773.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.055778 restraints weight = 42990.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056447 restraints weight = 27198.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056853 restraints weight = 20209.747| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26797 Z= 0.223 Angle : 0.580 11.366 36364 Z= 0.314 Chirality : 0.053 1.382 3900 Planarity : 0.003 0.057 4660 Dihedral : 4.508 58.188 3613 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 33.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.71 % Allowed : 21.13 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3270 helix: 0.25 (0.43), residues: 170 sheet: -0.88 (0.14), residues: 1330 loop : -1.43 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 21 TYR 0.020 0.001 TYR R 105 PHE 0.011 0.001 PHE T 66 TRP 0.011 0.001 TRP Q 67 HIS 0.005 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00483 (26780) covalent geometry : angle 0.58048 (36330) SS BOND : bond 0.00266 ( 17) SS BOND : angle 0.58078 ( 34) hydrogen bonds : bond 0.03834 ( 946) hydrogen bonds : angle 5.12423 ( 2370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 377 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 78 GLU cc_start: 0.9464 (mp0) cc_final: 0.8885 (mp0) REVERT: O 106 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8679 (m-10) REVERT: O 114 GLU cc_start: 0.9326 (mp0) cc_final: 0.8869 (mp0) REVERT: S 4 MET cc_start: 0.8757 (mmm) cc_final: 0.8432 (mmm) REVERT: A 78 GLU cc_start: 0.9412 (mp0) cc_final: 0.8860 (mp0) REVERT: A 106 TYR cc_start: 0.8757 (m-10) cc_final: 0.8398 (m-10) REVERT: A 125 THR cc_start: 0.9376 (m) cc_final: 0.9070 (p) REVERT: C 33 ARG cc_start: 0.9363 (mmt90) cc_final: 0.8824 (mmt90) REVERT: C 36 MET cc_start: 0.9350 (mmp) cc_final: 0.8749 (mmm) REVERT: C 82 TYR cc_start: 0.9084 (m-80) cc_final: 0.8708 (m-10) REVERT: C 106 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: E 78 GLU cc_start: 0.9415 (mp0) cc_final: 0.8894 (mp0) REVERT: E 106 TYR cc_start: 0.8808 (m-10) cc_final: 0.8102 (m-10) REVERT: G 78 GLU cc_start: 0.9491 (mp0) cc_final: 0.8893 (mp0) REVERT: G 114 GLU cc_start: 0.9140 (mp0) cc_final: 0.8845 (mp0) REVERT: I 36 MET cc_start: 0.7986 (mmm) cc_final: 0.7692 (mmm) REVERT: I 106 TYR cc_start: 0.8548 (m-80) cc_final: 0.8247 (m-80) REVERT: K 36 MET cc_start: 0.7909 (mmm) cc_final: 0.7462 (mmm) REVERT: K 62 TYR cc_start: 0.7265 (m-80) cc_final: 0.6686 (m-80) REVERT: K 85 MET cc_start: 0.8480 (mpp) cc_final: 0.7890 (mpp) REVERT: K 87 ASN cc_start: 0.9541 (m110) cc_final: 0.9263 (t0) REVERT: K 106 TYR cc_start: 0.8703 (m-80) cc_final: 0.8491 (m-80) REVERT: K 108 LYS cc_start: 0.3346 (OUTLIER) cc_final: 0.2912 (mmtm) REVERT: K 125 THR cc_start: 0.9342 (m) cc_final: 0.9123 (p) REVERT: M 85 MET cc_start: 0.8505 (mpp) cc_final: 0.8007 (mpp) REVERT: P 62 TYR cc_start: 0.7534 (m-80) cc_final: 0.7026 (m-80) REVERT: P 72 ILE cc_start: 0.7959 (tt) cc_final: 0.7576 (tt) REVERT: P 85 MET cc_start: 0.8729 (mpp) cc_final: 0.8279 (mpp) REVERT: R 21 ARG cc_start: 0.8735 (tpp80) cc_final: 0.8402 (tpp80) REVERT: R 85 MET cc_start: 0.8909 (mtm) cc_final: 0.8647 (mtm) REVERT: R 87 ASN cc_start: 0.9605 (m110) cc_final: 0.9310 (t0) REVERT: R 96 TYR cc_start: 0.8388 (m-10) cc_final: 0.8139 (m-10) REVERT: R 122 THR cc_start: 0.9017 (t) cc_final: 0.8427 (p) outliers start: 77 outliers final: 71 residues processed: 411 average time/residue: 0.3713 time to fit residues: 228.6284 Evaluate side-chains 449 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 375 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 161 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 40 optimal weight: 0.0970 chunk 38 optimal weight: 6.9990 chunk 295 optimal weight: 30.0000 chunk 197 optimal weight: 30.0000 chunk 284 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 193 optimal weight: 20.0000 overall best weight: 4.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.052906 restraints weight = 233370.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055087 restraints weight = 83316.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056338 restraints weight = 42032.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057013 restraints weight = 26491.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057391 restraints weight = 19567.313| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26797 Z= 0.164 Angle : 0.563 11.258 36364 Z= 0.304 Chirality : 0.053 1.369 3900 Planarity : 0.003 0.082 4660 Dihedral : 4.414 56.400 3613 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 31.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.57 % Allowed : 20.99 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3270 helix: 0.37 (0.43), residues: 170 sheet: -0.76 (0.14), residues: 1310 loop : -1.34 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 58 TYR 0.022 0.001 TYR R 105 PHE 0.011 0.001 PHE T 66 TRP 0.010 0.001 TRP Q 67 HIS 0.006 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00359 (26780) covalent geometry : angle 0.56329 (36330) SS BOND : bond 0.00187 ( 17) SS BOND : angle 0.44612 ( 34) hydrogen bonds : bond 0.03596 ( 946) hydrogen bonds : angle 5.05253 ( 2370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 384 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 78 GLU cc_start: 0.9475 (mp0) cc_final: 0.8892 (mp0) REVERT: O 106 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8614 (m-10) REVERT: O 114 GLU cc_start: 0.9363 (mp0) cc_final: 0.9090 (mp0) REVERT: S 4 MET cc_start: 0.8768 (mmm) cc_final: 0.8448 (mmm) REVERT: A 78 GLU cc_start: 0.9432 (mp0) cc_final: 0.8882 (mp0) REVERT: A 106 TYR cc_start: 0.8730 (m-10) cc_final: 0.8395 (m-10) REVERT: A 125 THR cc_start: 0.9375 (m) cc_final: 0.9067 (p) REVERT: C 33 ARG cc_start: 0.9370 (mmt90) cc_final: 0.8820 (mmt90) REVERT: C 36 MET cc_start: 0.9375 (mmp) cc_final: 0.8816 (mmm) REVERT: C 82 TYR cc_start: 0.9077 (m-80) cc_final: 0.8686 (m-10) REVERT: C 106 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: E 78 GLU cc_start: 0.9418 (mp0) cc_final: 0.8894 (mp0) REVERT: E 106 TYR cc_start: 0.8743 (m-10) cc_final: 0.7979 (m-10) REVERT: F 16 ASP cc_start: 0.9120 (p0) cc_final: 0.8428 (t0) REVERT: G 78 GLU cc_start: 0.9502 (mp0) cc_final: 0.8890 (mp0) REVERT: G 114 GLU cc_start: 0.9187 (mp0) cc_final: 0.8888 (mp0) REVERT: H 16 ASP cc_start: 0.9024 (p0) cc_final: 0.8246 (t0) REVERT: I 36 MET cc_start: 0.7957 (mmm) cc_final: 0.7678 (mmm) REVERT: I 62 TYR cc_start: 0.7828 (m-80) cc_final: 0.7284 (m-80) REVERT: I 106 TYR cc_start: 0.8458 (m-80) cc_final: 0.8212 (m-80) REVERT: K 36 MET cc_start: 0.7966 (mmm) cc_final: 0.7422 (mmm) REVERT: K 62 TYR cc_start: 0.7259 (m-80) cc_final: 0.6714 (m-80) REVERT: K 85 MET cc_start: 0.8529 (mpp) cc_final: 0.7927 (mpp) REVERT: K 87 ASN cc_start: 0.9541 (m110) cc_final: 0.9262 (t0) REVERT: K 106 TYR cc_start: 0.8748 (m-80) cc_final: 0.8527 (m-80) REVERT: K 108 LYS cc_start: 0.3289 (OUTLIER) cc_final: 0.2855 (mmtm) REVERT: K 125 THR cc_start: 0.9338 (m) cc_final: 0.9125 (p) REVERT: M 85 MET cc_start: 0.8572 (mpp) cc_final: 0.8014 (mpp) REVERT: P 62 TYR cc_start: 0.7549 (m-80) cc_final: 0.7057 (m-80) REVERT: P 72 ILE cc_start: 0.7924 (tt) cc_final: 0.7532 (tt) REVERT: P 85 MET cc_start: 0.8755 (mpp) cc_final: 0.8276 (mpp) REVERT: P 89 LYS cc_start: 0.8550 (mppt) cc_final: 0.8250 (mppt) REVERT: P 92 ASP cc_start: 0.9051 (p0) cc_final: 0.8774 (p0) REVERT: R 21 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8410 (tpp80) REVERT: R 85 MET cc_start: 0.8910 (mtm) cc_final: 0.8655 (mtm) REVERT: R 87 ASN cc_start: 0.9597 (m110) cc_final: 0.9308 (t0) REVERT: R 122 THR cc_start: 0.8935 (t) cc_final: 0.8298 (p) outliers start: 73 outliers final: 69 residues processed: 415 average time/residue: 0.3792 time to fit residues: 235.6160 Evaluate side-chains 451 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 379 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 161 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 252 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 167 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 231 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 chunk 215 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 296 optimal weight: 0.9980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 HIS H 95 HIS ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.080933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.053699 restraints weight = 231565.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055914 restraints weight = 81261.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.057147 restraints weight = 40825.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.057722 restraints weight = 25680.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058198 restraints weight = 19308.167| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26797 Z= 0.114 Angle : 0.547 11.264 36364 Z= 0.294 Chirality : 0.053 1.389 3900 Planarity : 0.003 0.059 4660 Dihedral : 4.194 54.373 3613 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 28.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.39 % Allowed : 21.20 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3270 helix: 0.52 (0.44), residues: 170 sheet: -0.66 (0.14), residues: 1310 loop : -1.21 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 58 TYR 0.020 0.001 TYR R 105 PHE 0.010 0.001 PHE T 66 TRP 0.009 0.001 TRP F 110 HIS 0.005 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00262 (26780) covalent geometry : angle 0.54743 (36330) SS BOND : bond 0.00128 ( 17) SS BOND : angle 0.35131 ( 34) hydrogen bonds : bond 0.03299 ( 946) hydrogen bonds : angle 4.91658 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7517.43 seconds wall clock time: 130 minutes 0.24 seconds (7800.24 seconds total)